sneumann
commented
7 months ago Hi, I don't think I have seen that specific error message so far.
The unable to load shared object indicates that a symbol for required shared *.so library can't be found, which typically happens if there are several versions and there is an inconsistency between the version from which the *.h header files and later the used *.so library occurs.
Using the c++filt tool I can demangle the cryptic symbol name:
echo '_ZNK2H510H5Location13createDataSetERKSsRKNS_8DataTypeERKNS_9DataSpaceERKNS_17DSetCreatPropListERKNS_15DSetAccPropListERKNS_17LinkCreatPropListE' | c++filt
H5::H5Location::createDataSet(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, H5::DataType const&, H5::DataSpace const&, H5::DSetCreatPropList const&, H5::DSetAccPropList const&, H5::LinkCreatPropList const&) constSo, my guess is that there are several versions of libhdf5 installations on that computer. Can you find more than one instance of libnetcdf.so e.g. in /usr/lib/.../libnetcdf.so and another one in /opt or your $HOME ?!
Can you provide the output of ldd /opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so ?
Look out for libnetcdf.so in the output.
Thanks, Steffen
wangshisheng
Dear sneumann,
When I installed the mzR package using "BiocManager::install("mzR")" in centos7/R 4.3.2, it gived me the error below: ... R inst byte-compile and prepare package for lazy loading help *** installing help indices converting help for package ‘mzR’ finding HTML links ... done copyWriteMSData html
isolationWindow-methods html
metadata html
mzR-class html
finding level-2 HTML links ... done
building package indices installing vignettes ** testing if installed package can be loaded from temporary location Error: package or namespace load failed for ‘mzR’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so': /opt/R/4.3.2/lib/R/library/00LOCK-mzR/00new/mzR/libs/mzR.so: undefined symbol: _ZNK2H510H5Location13createDataSetERKSsRKNS_8DataTypeERKNS_9DataSpaceERKNS_17DSetCreatPropListERKNS_15DSetAccPropListERKNS_17LinkCreatPropListE Error: loading failed Execution halted ERROR: loading failed
Below is my sessioninfo:
Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so; LAPACK version 3.8.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai tzcode source: system (glibc)
attached base packages: [1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached): [1] BiocManager_1.30.22 compiler_4.3.2 tools_4.3.2
Could you give some helps about this? Thanks a lot!
Shisheng